1ntq

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(New page: 200px<br /><applet load="1ntq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ntq" /> '''5'(dCCUCCUU)3':3'(rAGGAGGAAA)5''''<br /> ==...)
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Revision as of 21:40, 24 November 2007

Image:1ntq.gif

1ntq

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5'(dCCUCCUU)3':3'(rAGGAGGAAA)5'

Overview

The 1-propynylation at C5 of consecutive pyrimidines in DNA can enhance, DNA:RNA hybrid stability at 37 degrees C by over 1 kcal/mol of, substitution [Barnes, T. W., III; Turner, D. H. J. Am. Chem. Soc.2001, 123, 4107-4118]. To provide information on the structural consequences of, propynylation, two-dimensional NMR spectroscopy was used to study the, structures of several oligonucleotides. Intraresidue nuclear Overhauser, effect spectroscopy cross peaks were observed at 30 degrees C and a 200 ms, mixing time in the H6-H1' region for 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P)), (ssPrODN) but not for 5'(dCCUCCUU) (ssODN), suggesting preorganization of, the propynylated single strand. NMR structures of the duplexes, 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (PrODN:RNA), 5'(dCC(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (sPrODN1:RNA), and, 5'(dCCUCCUU)3':3'(rGAGGAGGAAAU)5' (ODN:RNA) indicate that their global, structures are almost identical. The NMR data, however, suggest that the, 5'-end of sPrODN1:RNA is more dynamic than that of PrODN:RNA. In the, propynylated duplexes, the propyne group stacks on the aromatic ring of, the 5'-base and extends into the major groove. The results suggest that, the increased stability of the propynylated duplexes is caused by, preorganization of the propynylated single strand and different, interactions in the double strand. The propynyl group provides volume, exclusion, enhanced stacking, and possibly different solvation.

About this Structure

1NTQ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

NMR studies of DNA single strands and DNA:RNA hybrids with and without 1-propynylation at C5 of oligopyrimidines., Znosko BM, Barnes TW 3rd, Krugh TR, Turner DH, J Am Chem Soc. 2003 May 21;125(20):6090-7. PMID:12785839

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